ClinVar Miner

Submissions for variant NM_080605.4(B3GALT6):c.545A>G (p.Tyr182Cys)

gnomAD frequency: 0.00001  dbSNP: rs1314046622
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001855715 SCV002294928 uncertain significance Ehlers-Danlos syndrome, spondylodysplastic type, 2; Spondyloepimetaphyseal dysplasia with joint laxity 2021-04-28 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has been observed in individual(s) with B3GALT6-related conditions ‚Äã(PMID: 29931299). ClinVar contains an entry for this variant (Variation ID: 624636) The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change replaces tyrosine with cysteine at codon 182 of the B3GALT6 protein (p.Tyr182Cys). The tyrosine residue is highly conserved and there is a large physicochemical difference between tyrosine and cysteine.
CeGaT Center for Human Genetics Tuebingen RCV003222124 SCV003916031 likely pathogenic not provided 2023-03-01 criteria provided, single submitter clinical testing B3GALT6: PM2, PM3, PS3:Moderate, PP4
OMIM RCV000766204 SCV000897635 pathogenic Ehlers-Danlos syndrome, spondylodysplastic type, 2 2019-03-29 no assertion criteria provided literature only

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